One defining characteristic of the water molecule is its polar nature. Polarity occurs when there is an uneven distribution of charges on the two ends of any molecule. In water, the oxygen atom is much more electronegative than each of the two hydrogen atoms covalently bonded to it. As a result, electrons are more highly attracted to the oxygen atom due to the oxygen's high affinity for the electrons, resulting in a net negative charge on the oxygen atom and a net positive charge on each of the hydrogen atoms. This unequal distribution of charges on each atom produces a net dipole moment in all water molecules, creating the basis for hydrogen bonding.

When the negatively charged oxygen atom in water attracts surrounding positively charged hydrogen atoms, a weak intramolecular force arises called the hydrogen bond. This interaction between water molecules accounts for the various unique properties of water.

Because the intramolecular force between the water molecules are weak, water has a very low melting point, boiling point, surface tension and heat of vaporization compared to others common solvents. In addition, the unique networkings of the Hydrogen bonds in water give it more unique properties including: High dielectric constant (the ability of water molecules to surround ions and diminish the attraction of opposite charges for each other), solid state is less dense than liquid state and thus has a negative volume of melting.

Protons tunnel across a series of hydrogen bonds between hydronium ions and water molecules

A water molecule is capable of forming a maximum of four hydrogen bonds due to its four bonding sites. Each hydrogen atom is able to form a hydrogen bond with surrounding oxygen atoms, and each oxygen atom is able to form two hydrogen bonds with surrounding hydrogen atoms because of the two lone pairs on the oxygen atom.

Although hydrogen bonds are weaker than the covalent bonds that hold the structure of the water molecule together, they are nonetheless responsible for various unique physical properties of water. Such properties include its relatively high melting and boiling point temperatures, accounted for by the collection of intermolecular forces between water molecules. Thus the hydrogen bonds require a high input of energy in order to break the bonds between molecules. Such weak bonds are crucial to biochemical systems; they are weak enough to be reversibly broken in biochemical processes, yet they are strong enough, when many form simultaneously, to help stabilize specific structures such as the double helix.